Ana2 command controls the channel selection and display features of the second analog channel. (The second analog channel is plotted as Y in X-Y plots.) Choosing an analog channel of zero, or setting the analog channel off, disables all processing of the second analog channel.  The display feature options are for the trial-by trial display of the second analog data. 

•Example

ana2 size 30
·See Also

Creating, printing and saving plots, Analog, Av2Analog, Frequency, Layout parameters, Set sort reverse,  Smo2, Trials, XY

Analog command controls the primary analog channel.  The primary channel is the channel used as X for X-Y displays.  The options are:

analog show

Creating, printing and saving plots, Ana2, AvAnalog, AvFirstDx, AvSmooth, FirstDx, Layout parameters, Set sort reverse, Smooth, Trials, XY

Append opens an existing file for writing with the Write command. Data written to the file is added to the file after the existing data. See the section on Protocol scripting files for more details.

append stats.txt

Close, Exporting results, Open, Write, Protocol scripting files

AutoUpdate forces MatOFF to update the current plot each time a parameter is changed.  It does not matter if the parameter is changed by a typed command or via the GUI.  Commands that would not change the graph do not cause the graph to update.  AutoUpdate stays in effect until the ManualUpdate command is given.

auto
window 2000        Plot will update immediately after this command

ManualUpdate

AvAnalog creates and controls the display of a single trace that is an equally-weighted average of all the first analog channel data.  Only the trials currently selected for display are included in the average.  The options are:

avanalog show

Creating, printing and saving plots, Analog, Layout parameters, Trials

Av2Analog creates and controls the display of a single trace that is an equally-weighted average of all the first analog channel data.  Only the trials currently selected for display are included in the average.  The options are:

av2analog show

Creating, printing and saving plots, Analog, Layout parameters, Trials

AvFirstDx layout command controls the calculation and display of a single trace that is an average of the first derivative of each trial of analog data. The options are:

avfirstdx show

Creating, printing and saving plots, Analog, AvAnalog, FirstDX, Layout parameters, Trials

Avsmooth command controls the calculation and display of a single trace that is an average of the smoothed analog trials for the first analog channel. Only the trials that meet all display criteria are included in the average. The options are:

Creating, printing and saving plots, Analog, AvAnalog, FirstDx, Layout parameters, Smooth, Trials

The Axis command controls the X axis of the plot.  It has saveral main parameters: xatzero, units, multiplot, subplot.  Xatzero controls the zero of the x axis.  Normally, zero time is aligned on the centering code.  When xatzero is turned on, zero time is aligned on the left edge of the plot.  All times become positive.  Multiplot allows up to 72 graphs on one plot.  Use the subplot parameter to choose which position the next graph will be placed.

 The options are:

subplot position numbering scheme:

2 plots/page

3 or 4 plots/page

5, 6, 7, or 8 plots/page

9, 10, 11 or 12 plots/page

13 to 24 plots/page

25 to 48 plots/page

49 to 78 plots/page

axis xatzero on

Creating, printing and saving plots, BinWidth, Segment, Plot

The Batch command simulates the DOS batch command for processing many different data files.  It recognizes a few special commands and sends all unrecognized commands to the DOS interpreter.  Batch supports DOS "replaceable parameters" (e.g., %1, %2, etc.).  It can also issue a Call to another batch file, but cannot be nested beyond the first Call command.  See the Protocol scripting files section for more details.

Commands processed by Batch:

batch monday.bat

The file "monday.bat" contains:

set makdat=8o
pcoff daily_recoding.pro day25 unit3 dummy [23-24] d25

Bell sends a beep sound to the operator. It is most useful in a protocol scripting files.

bell

The Break is strictly a protocol file command. It pauses protocol file execution and waits for the operator to enter commands. The operator can issue any MatOFF commands. Then, the protocol file can be continued. The Continue command is used to return to the pending protocol file.

file rgb
unit rgb10
break
show

This is a protocol file to open a file, set the unit and discontinue processing. The Continue command will resume processing with a Show command.

Continue, Quit, Protocol scripting files

The width of the histogram bins are set by the BinWidth command. The BinWidth value is either the number of pixels per bin or the number of milliseconds per bin, as set by the Axis command.

axis units absolute
histogram show
win 6000
bin 30
show

Display 6 seconds of histogram data with 30 ms bins.

Axis, Histogram, Window

The Windows pop-up calculator can be accessed with the Calculator command. 

calc

Cd acts like the DOS change directory command.

cd ..

Take one step down the directory tree.

Dir, Pwd

One of the primary functions of MatOFF is to search through the data and find trials that are related to each another based on the search criteria. The selected trials must be aligned in time on some common event. The Center command identifies the event for alignment. Actually, it does not identify an event, per se. It identifies which bracketed group of events in the search sequence to use for alignment. Alternatively, the value can identify a history class that contains the absolute time (in milliseconds) in each trial to use as the alignment point for that trial. 

The center value indicates a event code group when the value is less than or equal to the number of groups in the sequence:

seq [14][3][28-30][33]
center 3
mark 4
show

The above sequence has 4 groups of event codes. The command "center 3" indicates that the third sequence element ([28-30]) will be used for centering. All trials will be aligned on whichever code (28, 29, or 30) was found when a trial matched the search criteria. In this case 28 was a "go left", 29 was a "go right", and 30 was a "go down". All trials will be centered on the "go" signal, regardless of the direction of the "go" signal. The operator must be careful not to confuse event codes with the ordinal number used in the Center specification. Thus, "center 3" does not mean to center on code "3"; it means to center on the third group of codes.

If the center value is above 99 (and if there are fewer than 99 groups), then the center value indicates a history class. The class value for each trial will be used as the centering time (in milliseconds). Centering on a class is one of the many advanced features of history scripting.

seq [14][3][28-30][33]
center 200
mark 4
history file centering_script.m
history on
scan
show

The above example uses history class 200 for the centering values. The history script "centering_script.m" sets the centering time for each trial and saves that value (in milliseconds from the start of the trial) in class 200. The plot will reflect the new centering times.

GlobalIgnore, History Scripting, Mark, Sequence, Shift, Sort Center, Sort Epoch, Sort Time, Spot

CenterLine layout command controls the display of a vertical line centered at the centering code.

If an abbreviated form of the CenterLine command (e.g., center) is accidentally used without including any parameters, MatOFF will interpret the command as a Center command.

center show

Center, Layout parameters,

The Clean command closes all open MatOFF files (protocol, metafiles, data files, etc.). It is used primarily for debugging after a MatOFF error leads to a MATLAB prompt.

clean

·See Also

Errorlevel

Close will close a currently open ASCII text file or data file.

Close with no parameter will look for an open ASCII text file and close it.  If there is no ASCII file open, it will close the currently open data file.  Close ascii will close a file that was opened with either Open or Append commands.  Close datafile will only try to close a currently open data file.  Close append will close all open SET <process> APPEND files.  

set epoch keep
append stats.txt
show
close ascii

Append, File, Open, Set, Write, Protocol scripting files

Cmd leaves the MATLAB command line and returns control to MatOFF.  Return to the MATLAB command prompt by entering the Matlab command.

>matlab
» !copy koflay.dat oldlayout.dat
» cmd
>

In this example we use MATLAB to make a backup of the koflay.dat layout file, then return to MatOFF.

When a protocol file issues a Break command, control of MatOFF goes to the user's keyboard. the user may resume the protocol file at any time with the Continue command. If a new protocol file is loaded, the Continue command becomes invalid until a new Break command occurs. If Fileerror has been issued with the break option, then any error caused by a File command will mimic a Break command. The Continue command can then be used to resume processing.

continue

Continue processing the protocol file.

Break, File, Fileerror, Load, Protocol scripting files

A layout is a detailed description of the elements to place on a plot. Ten layouts reside in MatOFF at any one time; only one layout is in use at any given time. The parameters of one layout can be copied to another layout using the Copy command. The origin and destination are simply the layout numbers (1..10). Text is handled separately. To copy text the Copy command must include the "text" keyword. Line numbers after the text keyword indicate which lines of text to copy. Omitting the "text lines" parameter will cause all text lines to be copied.

copy 4 5

Copy all parameters from layout 4 to layout 5.

copy 1 2 text

Copy only the text from layout 1 to layout 2.

Creating, printing and saving plots, Layout, Display, Show, Text

The Date command prints the current date.  In a protocol you can use the variable %10 for the current date.

date

Time

Directory is similar to the DOS DIR command. It will display the contents of a disk directory. If no path is specified, the current default path is used (not the DEFAULTPATH environmental variable value). If no file extension is given, none is assumed.  Ls is a synonym.

dir c:\matoff

Cd, Pwd

Whenever the Show, New plot, or Old plot command is given without parameters, the display list is used to select which layout(s) will be used for graphical display. If the display list has only one number, that layout will be used. If the display list is larger, the same data set will be displayed once for each layout. Note that the Display command does not initiate the display of data, it only sets the layout list for the Show command. The list may include ranges (e.g. 1-3), but it must be limited to values between 1 and 10. The display list can also be changed by the Show command.

display 1,3

Use layouts 1 and 3 next time the Show command is issued without parameters.

Show, Layout

Dump will print or save to disk information that has been gathered, organized, or calculated by MatOFF.  The general form of the Dump command is:

dump <datatype> [OUTPUT] <filename> 

The data types are listed below.   "OUTPUT" is a keyword.  It indicates that the data should be sent to the printer or a file. OUTPUT is always followed by the filename.  The Dump command is a simplified way to get internal values from MatOFF.  However, see the Set command, which is the primary method for moving data to other programs.   Both are detailed in Exporting results.

Dump spikes

Spike times are listed for the trials that match the sequence, and in the order based on current sort option.  The spike times are all in milliseconds relative to the centering code.  On the screen, spikes are dumped as one spike time per line.  With the [OUTPUT] option, spike times are listed this way:

sorted trial number  :unsorted trial number  :time,time,time

1 :15 :1336,1427,1430,1693
2 :21 :720,1752,1754,1916,3260,3514,3528,3530,3561,3573,3574,3593,3608,3611,3655,3657,3694,3976,3978,4214,
3 :24 :1450,1498,1512,1571
4 :23 :776,1732,1734,1781,1793,1857,5074,5471
5 :25 :768,785,1777,1785,1813,1838,6104,6106,6213,6215,6572,6573,7179,7199,7201,7248,7249

Dump spikes uses three environmental variables:

dump index OUTPUT index.txt

Print the index of the currently opened file to a text file.

dump set

Show the current settings of all the Set command options.

Exporting results, Found, History Scripting, Index, Segment, Set, environmental variables

Edit opens a windows text editor.  The editor is specified in the EDIT environmental variable.

The environmental variable EDITOR must be set before using this command. •Example

setenv editor c:\windows\notpad.exe
edit listfile.lst

Setenv, Environmental variables

End terminates the execution of a current protocol file. It will also terminate the execution of the current metafile.  If the metafile is called by a protocol file, using End in the metafile does not affect the execution of the protocol file.

file darby
unit db0001a
end                 <---- terminate the protocol file early (for testing)
sequence [12][22][35-38][42][44]
show

Endif, Protocol scripting files

The ENDIF command terminates a protocol file if the condition is met. The ENDIF command can only be used in a protocol file. It will be echoed, but have no effect in a metafile or on the command line.

This is in a protocol file:
file RY001_2a
unit RY2a
ENDIF NOUNIT       <---- end the protocol file if no unit was found
analog 3
ENDIF NOANALOG     <--- end the protocol file if there is no analog data
ana2 4
sequence [14][18][22-26][29][33]
show

Erase clears the graphics screen. It can be used with Axis multiplot to clear the plot for a new group of graphs.

erase

Creating, printing and saving plots,Axis

ErrorLevel controls the reporting of errors and warnings. 

The debug level of error messages provides the most information. The fatal level of error messages prevents all messages except for program failures.  The serious level of error messages can be used with batch files to suppress long lists of commands (e.g. layout commands), since errors are often missed when many commands are send to the screen. All of these messages can be sent to a log file.  See the Log command.  History scripting can make use of the same ErrorLevel control by using the issue_message() support function.

The Makdat command has a separate set of message reporting options.

error serious

Turn off warnings.

Log, Makdat

Exit MatOFF and MATLAB immediately, without confirmation. It is different from the Quit command, which keeps MATLAB running. 

When MatOFF exits, it saves the current set of layouts to the file koflay.dat.

exit

·See Also

Quit, Break, Protocol scripting files, Layouts

File opens a new data file for analysis. If no path is specified, the DATAPATH environmental variable is used. If DATAPATH is not assigned, DEFAULTPATH is used. If the File command is issued with no arguments, MatOFF will print the file name of the currently open file.  If the File command is issued with the same name as the currently open file, MatOFF will just issue a warning message. Otherwise, the File command will close the currently open file and attempt to open the new one.  To close and open files of the same name, issue the Close command first. A file cannot be opened unless it is a MatOFF file.  Use Makdat to process Cortex files for use with MatOFF.  See Importing for more information.

file indy

Close, Fileerror, Index, Makdat, Read, Unit

Fileerror tells MatOFF what action to take if a File command fails during the execution of script (protocol or metafile) file. If a File command is issued from the command line, or with a mouse, an error message is printed on the user’s screen. If a File command is issued in a script, there are three possible actions depending upon the most recent Fileerror command. The Fileerror command options are:

 The Fileerror exit form of the command is intended to be used with the Pcoff command.  The Pcoff command can only used inside a batch file using the Batch command.  Fileerror exit causes an abort of the current Pcoff command, which allows the batch file to continue. If Fileerror break is used and a file error occurs, then the Continue command can be used to resume processing of the protocol file.

fileerror exit
batch indyunits.bat

If MatOFF cannot find a data file during a Pcoff command within the indyunits.bat file, MatOFF will move to the next batch command in that file.

File, Batch, Break, Continue, Pcoff

FirstDx layout command controls the calculation and display of traces that are first derivatives of the analog data for each trial. The options are:

FirstDx only operates on the primary analog channel.

firstdx show

Creating, printing and saving plots, Analog, Layout parameters

Found prints a list of the sequences that matched the search criteria during the most recent scan.  Each matching sequence is listed once.  The sequence list is preceded by a number that indicates how many trials were found with that exact sequence.

>found
Qty   Sequence
 6    65 98 65 44 87 47 41
 6    65 99 65 42 87 46 41
 5    65 98 65 44 87 46 41
 1    65 98 65 43 87 47 41

·See Also

Sequence

If analog data are included in any analysis, it is essential to tell MatOFF the frequency that the analog data were collected. Any integer value can be entered, but it must match the frequency of the data for the selected analog channel. If two channels have been selected by the Analog command, both channels are assumed to be digitized at the same rate.

analog 1
freq 250

analog 1
seq [198][100][20][40][101]
glo auto 1-500
scan
freq auto 250 500 1000

The first example tells MatOFF to use analog channel 1, and to indicate that channel 1 was recorded at a frequency of 250 Hz.  The second example tells MatOFF to select an A/D rate of 250, 500, or 1000, based on the calculated A/D rate.  Before you can use the auto option, you must have a successful scan.  The sequence must include the A/D start and stop event codes (default are 100 and 101).  The A/D rate estimate is best when at least 20 trials are found. 

If you are using Cortex to collect the data, the A/D storage rate setting in Cortex corresponds to the following sampling frequencies listed below.  The table assumes only 2 channels of A/D data are being collected (i.e., EOG but not EPP data).  

·See Also

Analog

GlobalIgnore identifies event codes that are to be completely ignored during the event search and all subsequent analyses.  

global [1-10,12-15,33]

Instructs MatOFF to act as if the listed event codes do not exist in the data file.

sequence [23][30][45][46]
global auto [10-300]

These two commands will automatically create a global ignore list that looks like:
[10-22,24-29,31-44,47-300]

Sequence

The Hair command enables the mouse to precisely measure time values in a plot window.  Left click the mouse to drag a marker within the plot window. Let up on the mouse button to measure the precise time location of the marker.  Time is given in PCOFF pixels or in absolute time dependend on the Axis units command setting.

hair
Locate a position on the plot with the mouse.
781 milliseconds

MatOFF will include six lines of information on the graphics display as a heading. The information includes the file, unit name, search sequence, globalignore list, etc.

heading show

Creating, printing and saving plots, Text, Layout parameters

The Help command is available for on-line assistance.  A list of topics can be obtained by entering "help".  The HTML documentation is more complete.

help sequence

Find out more about the Sequence command.

The Hide Plotcommand inhibits the screen drawings (plots) when the Show command is given.  This command is most useful during batch file operation when statistical outputs are of interest, but drawings are not.  The reverse command is Show plot (a synonym for Set plot show).  

hide plot
load bigjob.pro

Set plot noshow

Histogram layout command controls the display of a cumulative histogram of spike data.  The histogram displayed by MatOFF is based on those trials that meet all the search and display criteria.  That is, all trials that would be shown if a Raster Show command is issued.Histogram values can be further restricted to specific parts of each trial using the ValidateSpikes command.   The bin sizing of the histogram is controlled by the BinWidth command. The MatOFF Scale command is the same as the Histogram scale command. Normally, the scaling of the histogram is relative to the bin width and the number of trials to provide a normalized pulses-per-second value.  If Histogram raw command is used, scaling is calculated from the number of counts in each bin independent of the bin width or number of trials.  Histogram reference commands will draw three horizontal reference lines on the histogram.  One line will be the average firing rate for all bins that fall completely within Segment A (see >Segment command). The other two lines will be above and below this mean based on the reference value.  The reference value is the number of standard deviations above and below the mean for these two lines.

histogram show

BinWidth,Layout parameters,Scale, Segment, RIP

The history command provides is a powerful method to make decisions about behavioral events.  See History Scripting for details.

history file myscript.m
history on
show

Dump, History Scripting

Index lists the data file index, which contains a list of what units are contained in the current file.

>file sparky25
>index

Find out what units are in file "sparky25".

Dump, File, Makdat, Show Spikecounts, Unit

Initialize resets all layout parameters of the currently-selected layout to a standard default set. It is used primarily in protocol files to set the layout to a known state.  See Layouts section for more details.

>init

Displays, Layout

Ten layouts reside in MatOFF at any one time.  A plot is drawn based on the currently selected layout. The current layout can be modified using either typed commands or through the layout menus. The Layout command allows the user to select which layout is current. A new set of 10 layouts can be loaded from a file using Layout file form of the command. If the Layout file command opens a new file, all layouts will be initialized to default values.  The existing layouts can be saved using Layout save .  The current set of layouts is automatically stored as koflay.dat when MatOFF is exited. This file may be copied and loaded with the Layout file command. The currently selected layout can be preserved as a protocol file using the Save layout command. 

layout file indylay.dat
layout 5
avanalog show
show 5

This example opens a layout file, makes layout 5 current, turns on the average analog trace, then displays the current search data using that layout.

Copy, Initialize, Layout parameters, Save, Display

Load reads and executes MatOFF commands from a text file. The text file is referred to as a protocol file, and usually has a. pro extension. If the PROTOCOLPATH environmental variable is set, it used to determine the directory of the requested protocol file. Files created with the Save command have the format of a protocol file. The protocol file STARTUP.PRO is automatically executed when MatOFF is first started.  Protocol files must follow certain rules described in the section on Protocol scripting files.

load rgb

Opens the protocol file RGB.PRO and executes each MatOFF command in the file.

Break, End, Continue, Save, Protocol scripting files, Environmental variables

Log sends error, warning, debugging and other information to a text file.  When logging, errors, warnings, and debugging messages do not reach the console, but all other messages do. Log always appends to any existing file. The file is placed in the default path.

open output.log
close ascii
log file output.log
errorlevel debug
log on
show
log off
log close

First two lines are a trick to erase an old log file "output.log" if it exists. Next line opens the log file. Log on starts the logging.  All error, warning, and debug messages will be appended to output.log and will not be displayed on the user’s screen. Other user screen messages will be sent to both the user screen and log file. Set [process] show output will not go to the log file. Log off is not really necessary here, since log close will also turn off logging. Log close is essential to save the data.

Errorlevel, Environmental variables,

Ls acts like the DOS DIR directory listing command.  The Directory command is a synonym. 

ls ..

List contents of the current directory.

Cd, Pwd

Makdat must be run on a CORTEX data before the data in that file can be processed by MatOFF.  See The Makdat Command.

Importing Data

ManualUpdate ends the effects of AutoUpdate. AutoUpdate makes MatOFF update the current plot each time a parameter is changed.  It does not matter if the parameter is changed by a typed command or via the graphical menus.  Commands that would not change the current plot do not cause an update.  

auto
window 2000        Plot will update immediately after this command
shift 500
manual

AutoUpdate

Usually the Show command is used to start or reprocess data after making a change to the search strategy. Show relies on context to determine where in the process sequence to begin. Map overrides the context sensitivity of Show and forces a new data mapping. The Map command is rarely used.

map

Accumulate, Scan, Show, Taint

Mark is used in conjunction with the Center command to identify two events in each trial that can be used for sorting of trials and for some trial-by-trial statistics. A square marker is placed immediately under each raster at the point in the raster that the marked code occurred. If rasters are not displayed, the marked event can still be used for sorting, e.g. sorting of analog traces.

seq [4][3][28-30][33]
center 3
mark 4
show

The above sequence has 4 groups of event codes. The command "mark 4" indicates that the fourth sequence element ([33]) will be marked. In the graphics display a solid square below each raster is used to identify the exact moment that the marked code occurred. Note that the Mark specification follows the same rules as the Center specification. The operator must be careful not to confuse event codes with the ordinal number used in the Mark specification. Thus, "mark 4" does not mean to mark code "4" in this case.

Center, GlobalIgnore, Sequence, Set EpochStats, Shift, Sort Center, Sort Epoch, Sort Time, Spot

Matlab leaves the MatOFF command line and returns control to MATLAB.  MatOFF commands issued via the MatOFF menus will still execute properly.  Return to the MatOFF command prompt by entering the Cmdcommand.

>matlab
» !copy koflay.dat oldlayout.dat
» cmd

In this example we use MATLAB to make a backup of the koflay.dat layout file.

Cmd

MenuPosition save saves the current screen arrangement of the main MatOFF menus.  The menu arrangement can be recalled using the MenuPosition load version of the command.  The user can save many different menu layouts and choose the most convenient arrangement as needed.  MenuPosition is also helpful for users who use different screen resolutions at different times. 

The menu arrangement is saved to the current default directory.  No file suffix is assumed.  The main menus are: File Menu, Sequence Menu, Plot & Print Menu, Layout Menu 1, Layout Menu 2, Layout Menu 3, and Text Menu.

>menu save best_for_search.mnu 
>menu load best_for_layouts.mnu

In this example the menus were optimized for searching and that layout was saved to a file using the .mnu suffix.  In the following statement a previously saved arrangement (best_for_layouts) was loaded.  The main menus were automatically reorganized and repositioned.

mgplx2ctx is a stand-alone, graphical MATLAB program for converting Plexon ".plx" files to Cortex data files.  It requires a recent version of MATLAB (R13 or later).

See the mgplx2ctx page for details. See Plx2ctx if you are using an older version of MATLAB.

mgplx2ctx

The Wilcoxon Mann Whitney Statistic is a powerful nonparametric test.  It is useful when the statistical assumptions inherent in t-tests are violated. The null hypothesis tested by this test is that the medians of the two groups are equal. A z-value that is large enough so that the null hypothesis is rejected indicates that the chance of the medians being from a common distribution is sufficiently small. The statistic is obtained by first ranking two sets of data as a combined set and then comparing the sum of the ranks in the two individual sets.

MWFiles compares two sets of pulse data. Pulse (spike) data are saved each time a Show command is issued after the Set MWU Keep command is given. The pulse data are always stored in two files: Ax.MWU and Bx.MWU. A and B represent the two time segments of the currently displayed data, specified with the Segment command. The value of x in the file names is from 0 to 9999. These values start at 0 and are incremented once each time a new pair of files are generated. The starting value can be changed with the Set MWU Filenumber command. The MWFiles command tests any two MWU files against each other. MWU files are saved to and recalled from the directory assigned to the STATPATH environmental variable, if set; otherwise, the DEFAULTPATH environmental variable is used.

The commands Set MWU Show and Set MWU NoShow control whether the results of testing the most recent Ax.MWU file with the most recent Bx.MWU file are displayed on the screen each time the Show command is executed.

axis units absolute
segment a -200 100
segment b 300 600
set mwu filenumber 0
set mwu keep
sort off
trials 1-10
show
trials 81-90
show
mwfiles a0 b0
mwfiles b0 b1

In this example a time window (segment a) is created that covers 200 ms before to 200 ms after the centering code.  This period is used as a control period in this experiment.  A second time window (segment b) is created to cover 300 ms to 600 ms after the centering code.  This period is the test period in this experiment. The rasters are placed in chronological order using Sort Off. The first 10 trials are selected with Trials 1-10.  Show displays these 10 trials and generates files A0.MWU and B0.MWU.  A0.MWU is the statistic for segement a, B0.MWU is the statistic for segement b.  The second 10 trials of the same recording are selected by using the Trials 81-90 command. This second group is viewed and two additional files A1.MWU and B1.MWU are created. A Mann Whitney U-test is performed first between the control and test periods for the first 10 trials.  This checks for significant firing rate change between the control period and the test period early in the recording.  A Mann Whitney U-test is then performed between the test period for the first 10 trials and the same period for the second 10 trials.  This looks for a change in the test period between trials recorded early and trials recorded later in the same file. 

Typical output display:

Significant= 0 m= 10 n= 21 z= 1.315

"Significant" will equal 1 if the null hypothesis can be rejected with a probability greater than 0.05 (two-tailed test).

Segment, Set, STATPATH environmental variable, a statistics textbook

New plot is a synonym of the Show command, except it will always make the plot in a new window.  Show uses the current window.  New plot will create multiple plots if the "display list" has more than one value. See the Show command for details.

new plot

Reprocess if necessary, then draw a plot in  a new window.

Creating, printing and saving plots, Display, Erase, MatOFF Scripting Language, Old plot, Overplot, Show 

Old plot is a synonym for Show, except it can be used to specify which graphics output window to use for display.  Old plot with no parameters has the same action as Show with no parameters. See the Show command for more details.  See Overplot for drawing twice on the same display.

axis subplot 1
axis multiplot 1
old plot 11
axis multiplot 2
old plot 12
axis subplot 2
shift 1500
show

Draw a plot in window 11.  Draw the same plot in window 12 side-by-side with another view of the same data (shifted 1.5 seconds).

Creating, printing and saving plots, Display, Erase, MatOFF Scripting Language, Overplot, Show, New plot

Open creates and opens a file for writing. The Write command moves ASCII data to that file. If a file with the same filename already exists on the disk, the file is overwritten by the Open command.  Use Append to add to an existing file.  See the section on Protocol scripting files for more details.

open stats.txt

Append, Close, Write, Exporting Results, Protocol scripting files

Overplot plots on top of an existing plot.  Normally, any existing plot is cleared first.  Overplot leaves the current drawing on the figure and adds to that drawing.  Overplot will only work properly if used on the most-recently created figure.  See Show for more details on what happens when a new drawing is requested.

center 2
show 1
display 2
center 5
overplot

This sequence will make a plot using layout 1.  A second graph, based on layout 2, is overlaid on the first.  The second plot has a different centering code and uses a different layout (layout 2). 

Creating, printing and saving plots, Display, Erase, Old plot, Show, New plot

The Pcoff command is used with the Batch command.  The Batch command simulates DOS batch file processing. The Pcoff command is used in  a batch file to load a data file, a protocol file, a unit, and a group of parameters in one batch file command line.

pcoff <protocol file> <data file> <unit> <pcoff param1> <pcoff param2> ...

See the section on Protocol scripting files for more details.

batch monday.bat

The file "monday.bat" contains:

pcoff daily_recoding.pro day25 unit3 [23-24] d25

This command runs the "daily_recording.pro" protocol script file using data from "day25".  It loads unit "unit3" and everywhere the parameter $1 occurs in "daily_recording.pro" the character string "[23-24]" is inserted (in this case, in a Sequence command).  Also, the character string "d25" is inserted wherever parameter $2 occurs in the protocol file.  

Plx2ctx is a stand-alone, command-line Windows program for converting Plexon ".plx" files to Cortex data files. 

See the Plx2ctx page for details. If you are using a recent version of MATLAB (R13 or later), use mgplx2ctx.

plx2ctx -mplx2ctx.map m01.plx m01        (This is done in a DOS Window)

Convert m01.plx Plexon file to one or more Cortex files using the plx2ctx.map mapping scheme.

Plot stores a figure (plot) to disk. Plot name can be fixed or numeric and automatically incremented. 

The figure number is the MATLAB figure number.  It is the same figure number as specified in the Old plot command.  The Set plot command and the GRAPHICSFORMAT environmental variable control the destination file and file format of the Plot command.

The Set plot keep command will save a plot to the hard disk each time a plot is created.  Set plot nokeep turns off this automatic process.

Naming the plot file

The Set plot name <filename> command sets the name of all subsequent plot files.  Plot file creation is destructive.  That is, it erases any existing file of the same name.

Automatic naming of the plot file

If the plot file has not been named, then the plot file names are numeric and generated automatically.  The first plot file is named 0.png.  Subsequent file names are 1.png, 2.png, etc.  The ".png" suffix depends on the graphics file type (see below).  If the plot file has been named, use the Set plot name <filename> with a blank filename to enable automatic naming.

Controlling the number used in automatic file naming

The Set plot filenumber <#>  command sets the number of the next file saved automatically.

Controlling the graphics file type that is saved to disk

The command Setenv GRAPHICSFORMAT <graphics type> sets the type of graphics file save to disk.  The available graphics types are:

Creating a web page from a plot

See the secton on Protocol scripting files for an example of how to automatically create a HTML files from plots.

set plot filename best_unit
setenv graphicsformat jpeg
plot

Creating, printing and saving plots, Print, Set, environmental variables

Print sends a copy of the graphics screen to the current default Windows printer.  It can optionally choose a different graphics screen.

new plot
print orientation landscape
print papertype a4
print

Creating, printing and saving plots, Plot, Set

Single-unit (spike) data can be collected on up to 25 different pulse channels (numbered 0 through 24). Only one channel of data can be studied at a time. PulseChannel specifies which channel to analyze. If an unused pulse channel is specified and a Show command is given, MatOFF will tell the user which channels have data. Also, the Index command can be used to list the available pulse channels.  Note that the Makdat command controls which pulse channels are converted from other file formats.  If you expect data from a pulse channel, but no data is there, see if that channel was properly requested in the Makdat "list" file.

pulse 1   Indicates pulse channel 1 will be used for analysis

pulse off   Indicates no pulse data will be studied. This is useful for studying only the behavioral aspects of an experiment.

Index, Makdat

Pwd acts like the DOS pwd command.

pwd

Cd, Directory

Many MatOFF processes are time-consuming. Q allows the user to interrupt a process. Q will interrupt a protocol file with prejudice.

show
q

Regardless of where MatOFF is in the Show process, the Q will interrupt the process and return control to the console.

Break

Quit exits MatOFF, but keeps MATLAB running.  It is different from Exit, which terminates MATLAB. 

When MatOFF exits, it saves the current set of layouts to the file koflay.dat.

quit

Exit, Q, Save, Layouts

The Raster layout command controls the display of spike rasters. When active, there is one spike raster for each trial of data. Spike rasters are composed of two horizontal lines of information. The first line has vertical tick marks, one for each spike. The second horizontal line has squares("o") or plus signs ("+") under them. A single square marks when in the trial the "mark" code occurs (see the Mark command). Plus signs indicate when in the trial a spot code was encountered (see the Spot command). There can be multiple spots in a trial. mark and spot marker sizes are controlled by the "labels" option value. The size of the vertical tick marks for each spike is controlled by the "size" option value.  The various sort commands control the order in which the rasters are displayed.  The Set sort command can reverse that order.

raster show

Layout parameters, Mark, Spot, Trials, Sort commands, Set sort

Read displays or saves detailed information about the current unit. 

read <options> out=<filename>
read <options> append=<filename>

Any number of options may be included in the command.  Only the first 3 characters of an option are necessary. Using 'out=' will create an ASCII file to the device listed under <filename> instead of displaying the results on the user's screen.  The 'out=' option will destroy the contents of an existing file with the same file name.  Using 'append=' will also write to a file, but will append to an existing file.

read all out=mydump.txt

Creates a file with all event codes, pulses, marks, and analog data.

read relevant out=events.txt

124,1,198,204,40,64,34,152,50,90,92,96,143,139,14,80,25,28,56,77,84,100,78,64,60,21,55,30,35,161,29,19
125,2,198,205,40,65,31,152,50,90,92,96,144,140,14,81,23,28,56,77,84,100,78,65,60,21,55,30,35,160,29,164,19
126,3,198,205,40,65,31,152,51,91,93,95,98,145,139,14,81,24,28,56,77,84,100,78,65,60,21,55,158,162,30,35,158,29,19
127,4,198,203,40,63,33,152,50,91,92,96,145,137,14,82,24,28,56,77,84,100,78,63,60,21,55,30,35,160,29,19,20,44,87,88
128,5,198,201,40,61,31,152,50,90,92,96,143,139,14,81,23,28,56,77,84,100,78,61,60,21,55,30,35,158,29,19,20,42,87,88
129,6,198,205,40,65,31,152,50,90,92,96,141,137,14,82,23,28,56,77,84,100,78,65,60,21,55,158,162,30,35,160,164,158,29

This is the output file from read relevant.  The first value is the source trial number for the file (see SourceTrials).  The second number is the ordinal number of the trial in this unit.  The remaining numbers in each line are the event codes (in order) for that trial. Any code included in the GlobalIgnore list will not be included in the output file.

Dump, Exporting results, File, GlobalIgnore, Sequence, Set, Unit

RIP layout command controls the display of a cumulative reciprocal interval plot of spike data.

rip show

Histogram, Layout parameters

The Save command creates a protocol file.  The file it creates is a snapshot of all the current settings.  Execution of the saved file using the Load command will return MatOFF to the same state it was in when the Save command was issued.  The graphical layout settings can be saved independently of the other settings depending upon with form of the Save command is used.  Save uses the default extension of .PRO. If the PROTOCOLPATH environmental variable is set, Save uses that path to determine the target directory.

save rgb layout

Saves all the current settings, including layout information, to the file RGB.PRO.

Load, PROTOCOLPATH environmental variable

Whenever a histogram is specified in the current layout, the current value of Scale is used to set its vertical range in impulses per second (ips). Scale Auto instructs MatOFF to use the maximum histogram bin value to set the scale range. The Scale command is the same as the Histogram scale command.

window 6000
binwidth 120
scale 50
histogram show
show

Instruct MatOFF to plot histogram data for current data. Histogram will have 120 bins of 50 ms each (= 6 seconds of data), and have a full-scale firing rate of 50 pps

BinWidth, Histogram, Window

The Show, Old plot and New plot commands are normally used to start or reprocess data after making a change to the search strategy. These commands automatically decide which processing steps are required before a plot can be drawn.  The Scan command overrides the automatic decision-making and forces a new scan for trials that match the search criteria. The Scan command is used to trigger the processing of History scripting.  

scan

Accumulate, History scripting, Map, Show

SecondDx layout command controls the calculation and display of a traces that are second derivatives of the analog data for each trial. 

seconddx line <type> line type for trace
seconddx xpos x x position of trace in pixels
seconddx ypos y y position of trace in pixels
seconddx separation x number of pixels between traces. A negative value reverses the order of display
seconddx size x vertical size in pixels for trace

SecondDx only operates on the primary analog channel (see AnalogChannel command).

seconddx show

Analog, Creating, printing and saving plots, Layout parameters, Trials

There are several statistical calculations which can be made by MatOFF. Two of them, segment statistics and Mann Whitney U are based upon comparison of spike density between the two raster segments, "A" and "B". These segments are time periods marked-off on the graphics display. Their boundaries are specified in pixels using the Segment command. The time scale on the graphics display can be mapped onto 600 screen pixels for backwords compatibility with the old PCOFF program.  Otherwise, values are specified in absolute time (milliseconds) across the X axis.  The units are selected by the Axis command.  Two different segments can be defined simultaneously to make intra-trial calculations easier.  Once segments are set the user can extract information about those segments using the Dump segments command, or the Set segmentstats command.

The format <value>-<value>, (e.g., 300-400) is allowed if Axis units< is set to PCOFF.  This form of the command is for backwards compatibility, but cannot work with absolute units.  With absolute units the dash would be interpreted as a minus sign. The mouse can be used to select the segment value in the a1, a2, b1, and b2 versions of the command. 

shift 0
window 3000
axis pcoff
seg a 200 300
seg b 300 320
set segstats show
show

Using the old PCOFF mapping, define segment A as the 500 ms period before the centering code, and segment B as the first 100 ms after the centering code. After the Show command, spike counts for each trial, and descriptive statistics for these two window periods, will be listed on the console.

Axis, Dump, MWUFiles, Set

Sequence is one of the most important commands in MatOFF. It sets the search strategy for identifying trials (epochs) of interest. The sequence is composed of a series of event codes based on the event codes inserted into the data stream by the data collection or data conversion program. Event codes are grouped in brackets. Within a bracket, codes are logically ORed. Between brackets, codes are logically ANDed in temporal sequence. Thus the sequence: [23,24][25][26] means to search for a 23 or a 24, followed by a 25, then a 26. Two difference code sequences can satisfy this requirement: 23 25 26 and 24 25 26. Note that the sequence 23 15 25 26 is not acceptable. The code 15 interrupts the specified sequence and thus the trial would be rejected. Likewise, the sequence 23 24 25 26 would also be rejected, because code 24 interrupts the sequence. It is possible to "ignore" an intervening code. The way to ignore a code is to "globally" ignore it using the GlobalIgnore command.

seq [1][2,3][15-19][9]

MatOFF will look through the data for each sequence of codes which satisfy this specification. For example, if the codes 1 3 17 9 were encountered in the data stream in that order, uninterrupted by other codes, data for the trial will be accepted for analysis and display.

To ease typing, MatOFF tries to be as "open-minded" as possible when it comes to entering the Sequence command. The above sequence can be entered with:

seq 1] 2,3] 15-19] 9]

Center, GlobalIgnore, Mark, Span, Spot

The Set command is a powerful method for saving data after each search.  This is the primary method MatOFF uses for exporting data to other programs.  Set is also used to enable or disable some built-in features of MatOFF.   When used for saving data, the Set command prints or saves onto the disk each time a Show, Old plot, or New plot command is issued.  Thus, the Set command automatically stores results each time a plot is created.  Set is a rather complex command with multiple options and special files to define the ASCII format of any files that are saved.  See Exporting results for important details on using the Set command. Dump Sets can be used to display the status of many set "processes". 

The Set commands for moving data to the screen have the general form:

The Set commands for moving data to the hard disk have the general form:

DUMP LABEL 
15-Sep-2000        15:27:41
TRIAL  SEG-A   SEG-B
 108       8      30
 117      12      13
 135      10      22
 148      20      23
 157      12      28
 190      24       7
  10      21      22
  15      22      26
  60      20       5
  67      18      24

     |  SEG-A  SEG-B
-----+------------------------
  N  |    10      10